Subjective well-being (SWB) is a basic component of the health of children and adolescents. Studies of SWB in gifted students are scarce and show contradictory results. Some researchers consider these groups to be vulnerable, and according to some reports they are more often involved in situations of harassment as victims and/or harassers. Emotional intelligence (EI) is related to SWB and can be a protective factor in these situations. However, the underlying mechanism remains relatively unexplored, especially in the affective dimension of SWB. The present study develops and tests a model for the mediating role of mood in the relationship between EI and SWB. The participants were 273 Spanish students aged 8 to 18 years, distributed into two samples: sample 1, gifted students, and sample 2, unidentified students. The results showed that (1) gifted students exhibited lower scores in EI (specifically, in clarity) and SWB (specifically, in positive experiences) and higher scores on the sadness dimension of mood states and that (2) EI was positively related to SWB, and mood was a significant mediator in the relationship between EI and SWB. The mediating role of the positive mood is given in both groups; however, the negative mood only mediates this relationship in gifted students. The results are discussed, theoretical and practical contributions to the literature are proposed, and implications for parents and teachers are suggested.